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MINOR CONFORMER OF A BENZO[A]PYRENE DIOL EPOXIDE ADDUCT OF DA IN DUPLEX DNA
SOLUTION NMR
NMR Experiment
Experiment
Type
Sample Contents
Solvent
Ionic Strength
pH
Pressure
Temperature (K)
Spectrometer
1
NOESY
76 mM
6.8
1 atm
288
2
ROESY
76 mM
6.8
1 atm
288
3
TOCSY
76 mM
6.8
1 atm
288
4
2D EXCHANGE-ONLY SPECTRA
76 mM
6.8
1 atm
288
NMR Spectrometer Information
Spectrometer
Manufacturer
Model
Field Strength
1
Varian
UNITYPLUS
750
2
Varian
UNITYPLUS
600
NMR Refinement
Method
Details
Software
RELAXATION MATRIX REFINEMENT OF NOE DISTANCE RESTRAINTS AND RESTRAINED MOLECULAR DYNAMICS WITH SIMULATED ANNEALING
THE FOLLOWING RESTRAINTS WERE APPLIED IN THE MOLECULAR
DYNAMICS/ENERGY MINIMIZATION CALCULATIONS: (1)
INTER-PROTON DISTANCE RESTRAINTS DIRECTLY DERIVED FROM
RELAXATION MATRIX ANALYSIS OF NOE DATA; (2) IMINO PROTON
HYDROGEN BOND RESTRAINTS FOR ALL BASE PAIRS EXCEPT THE
CENTRAL DA-DG MISMATCH PAIR. THE MODIFIED DA RESIDUE OF
THIS MINOR CONFORMER DISPLAYED A C2'-ENDO SUGAR PUCKER AND
AN ANTI GLYCOSIDIC BOND. IT FORMED AN ANTI:ANTI BASE PAIR
CONTAINING TWO HYDROGEN BONDS WITH THE OPPOSITE DG. THE
MODIFIED DA RESIDUE OF THE MAJOR CONFORMER OF THIS
MOLECULE [YEH ET AL. (1995) BIOCHEMISTRY 34, 13570-13581]
DISPLAYED C3'-ENDO SUGAR PUCKER AND A SYN GLYCOSIDIC BOND.
THE MAJOR CONFORMER MODIFIED DA RESIDUE FORMED A SYN:ANTI
BASE PAIR CONTAINING NON-WATSON CRICK HYDROGEN BONDS WITH
THE OPPOSITE DG.
MORE REFINEMENT DETAILS CAN BE FOUND IN THE PRIMARY JOURNAL CITATION (SCHWARTZ ET AL.,1997).
Amber
NMR Ensemble Information
Conformer Selection Criteria
Conformers Calculated Total Number
1
Conformers Submitted Total Number
1
Representative Model
1 (minimized average structure)
Additional NMR Experimental Information
Details
MINIMIZED AVERAGE STRUCTURE. THE STRUCTURE WAS DETERMINED USING DISTANCE RESTRAINTS DERIVED FROM 2D NOESY EXPERIMENTS DONE IN 99.999% D2O AND 90% H2O/ 10% D2O. 2D ROESY, TOCSY, AND EXCHANGE-ONLY EXPERIMENTS WERE USED IN THE CHEMICAL SHIFT ASSIGNMENT PROCESS.